[INFO   ] Starting gmx_MMPBSA v1.5.2
[DEBUG  ] WDIR          : /media/romi/My Book Duo/completed-simulation-oracle/auto-immune/rs3/completed/2xwt-rs3-310k/free-energy
[DEBUG  ] AMBERHOME     : /home/romi/anaconda3/envs/gmxMMPBSA
[DEBUG  ] PYTHON EXE    : /home/romi/anaconda3/envs/gmxMMPBSA/bin/python
[DEBUG  ] PYTHON VERSION: 3.9.12 (main, Apr  5 2022, 06:56:58) [GCC 7.5.0]
[DEBUG  ] MPI           : /home/romi/anaconda3/envs/gmxMMPBSA/bin/mpirun
[DEBUG  ] ParmEd        : 3.4.3
[DEBUG  ] OS PLATFORM   : Linux-5.15.0-76-generic-x86_64-with-glibc2.31
[DEBUG  ] OS SYSTEM     : Linux
[DEBUG  ] OS VERSION    : #83~20.04.1-Ubuntu SMP Wed Jun 21 20:23:31 UTC 2023
[DEBUG  ] OS PROCESSOR  : x86_64

[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ci index.ndx -cg 18 19 -ct system_reduced.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[DEBUG  ] |Input file:
[DEBUG  ] |--------------------------------------------------------------
[DEBUG  ] |Input file generated by gmx_MMPBSA (v1.5.2)
[DEBUG  ] |Be careful with the variables you modify, some can have severe consequences on the results you obtain.
[DEBUG  ] |
[DEBUG  ] |# General namelist variables
[DEBUG  ] |&general
[DEBUG  ] |  sys_name             = ""                                             # System name
[DEBUG  ] |  startframe           = 10                                             # First frame to analyze
[DEBUG  ] |  endframe             = 19900                                       # Last frame to analyze
[DEBUG  ] |  interval             = 100                                         # Number of frames between adjacent frames analyzed
[DEBUG  ] |  forcefields          = "oldff/leaprc.ff99SB,leaprc.gaff"              # Define the force field to build the Amber topology
[DEBUG  ] |  ions_parameters      = 1                                              # Define ions parameters to build the Amber topology
[DEBUG  ] |  PBRadii              = 3                                              # Define PBRadii to build amber topology from GROMACS files
[DEBUG  ] |  temperature          = 310                                        # Temperature
[DEBUG  ] |  qh_entropy           = 0                                              # Do quasi-harmonic calculation
[DEBUG  ] |  interaction_entropy  = 0                                              # Do Interaction Entropy calculation
[DEBUG  ] |  ie_segment           = 25                                             # Trajectory segment to calculate interaction entropy
[DEBUG  ] |  c2_entropy           = 0                                              # Do C2 Entropy calculation
[DEBUG  ] |  assign_chainID       = 0                                              # Assign chains ID
[DEBUG  ] |  exp_ki               = 0.0                                            # Experimental Ki in nM
[DEBUG  ] |  full_traj            = 0                                              # Print a full traj. AND the thread trajectories
[DEBUG  ] |  gmx_path             = ""                                             # Force to use this path to get GROMACS executable
[DEBUG  ] |  keep_files           = 2                                              # How many files to keep after successful completion
[DEBUG  ] |  netcdf               = 0                                              # Use NetCDF intermediate trajectories
[DEBUG  ] |  solvated_trajectory  = 1                                              # Define if it is necessary to cleanup the trajectories
[DEBUG  ] |  verbose              = 1                                              # How many energy terms to print in the final output
[DEBUG  ] |/
[DEBUG  ] |
[DEBUG  ] |# (AMBER) Generalized-Born namelist variables
[DEBUG  ] |&gb
[DEBUG  ] |  igb                  = 5                                              # GB model to use
[DEBUG  ] |  intdiel              = 1.0                                            # Internal dielectric constant for sander
[DEBUG  ] |  extdiel              = 78.5                                           # External dielectric constant for sander
[DEBUG  ] |  saltcon              = 0.0                                            # Salt concentration (M)
[DEBUG  ] |  surften              = 0.0072                                         # Surface tension
[DEBUG  ] |  surfoff              = 0.0                                            # Surface tension offset
[DEBUG  ] |  molsurf              = 0                                              # Use Connelly surface ('molsurf' program)
[DEBUG  ] |  msoffset             = 0.0                                            # Offset for molsurf calculation
[DEBUG  ] |  probe                = 1.4                                            # Solvent probe radius for surface area calc
[DEBUG  ] |  ifqnt                = 0                                              # Use QM on part of the system
[DEBUG  ] |  qm_theory            = ""                                             # Semi-empirical QM theory to use
[DEBUG  ] |  qm_residues          = ""                                             # Residues to treat with QM
[DEBUG  ] |  qmcharge_com         = 0                                              # Charge of QM region in complex
[DEBUG  ] |  qmcharge_lig         = 0                                              # Charge of QM region in ligand
[DEBUG  ] |  qmcharge_rec         = 0                                              # Charge of QM region in receptor
[DEBUG  ] |  qmcut                = 9999.0                                         # Cutoff in the QM region
[DEBUG  ] |  scfconv              = 1e-08                                          # Convergence criteria for the SCF calculation, in kcal/mol
[DEBUG  ] |  peptide_corr         = 0                                              # Apply MM correction to peptide linkages
[DEBUG  ] |  writepdb             = 1                                              # Write a PDB file of the selected QM region
[DEBUG  ] |  verbosity            = 0                                              # Controls the verbosity of QM/MM related output
[DEBUG  ] |  alpb                 = 0                                              # Use Analytical Linearized Poisson-Boltzmann (ALPB)
[DEBUG  ] |  arad_method          = 1                                              # Selected method to estimate the effective electrostatic size
[DEBUG  ] |/
[DEBUG  ] |
[DEBUG  ] |# (AMBER) Possion-Boltzmann namelist variables
[DEBUG  ] |&pb
[DEBUG  ] |  ipb                  = 2                                              # Dielectric model for PB
[DEBUG  ] |  inp                  = 2                                              # Nonpolar solvation method
[DEBUG  ] |  sander_apbs          = 0                                              # Use sander.APBS?
[DEBUG  ] |  indi                 = 1.0                                            # Internal dielectric constant
[DEBUG  ] |  exdi                 = 80.0                                           # External dielectric constant
[DEBUG  ] |  emem                 = 4.0                                            # Membrane dielectric constant
[DEBUG  ] |  smoothopt            = 1                                              # Set up dielectric values for finite-difference grid edges that are located across the solute/solvent dielectric boundary
[DEBUG  ] |  istrng               = 0.0                                            # Ionic strength (M)
[DEBUG  ] |  radiopt              = 1                                              # Use optimized radii?
[DEBUG  ] |  prbrad               = 1.4                                            # Probe radius
[DEBUG  ] |  iprob                = 2.0                                            # Mobile ion probe radius (Angstroms) for ion accessible surface used to define the Stern layer
[DEBUG  ] |  sasopt               = 0                                              # Molecular surface in PB implict model
[DEBUG  ] |  arcres               = 0.25                                           # The resolution (Å) to compute solvent accessible arcs
[DEBUG  ] |  memopt               = 0                                              # Use PB optimization for membrane
[DEBUG  ] |  mprob                = 2.7                                            # Membrane probe radius in Å
[DEBUG  ] |  mthick               = 40.0                                           # Membrane thickness
[DEBUG  ] |  mctrdz               = 0.0                                            # Distance to offset membrane in Z direction
[DEBUG  ] |  poretype             = 1                                              # Use exclusion region for channel proteins
[DEBUG  ] |  npbopt               = 0                                              # Use NonLinear PB solver?
[DEBUG  ] |  solvopt              = 1                                              # Select iterative solver
[DEBUG  ] |  accept               = 0.001                                          # Sets the iteration convergence criterion (relative to the initial residue)
[DEBUG  ] |  linit                = 1000                                           # Number of SCF iterations
[DEBUG  ] |  fillratio            = 4.0                                            # Ratio between the longest dimension of the rectangular finite-difference grid and that of the solute
[DEBUG  ] |  scale                = 2.0                                            # 1/scale = grid spacing for the finite difference solver (default = 1/2 Å)
[DEBUG  ] |  nbuffer              = 0.0                                            # Sets how far away (in grid units) the boundary of the finite difference grid is away from the solute surface
[DEBUG  ] |  nfocus               = 2                                              # Electrostatic focusing calculation
[DEBUG  ] |  fscale               = 8                                              # Set the ratio between the coarse and fine grid spacings in an electrostatic focussing calculation
[DEBUG  ] |  npbgrid              = 1                                              # Sets how often the finite-difference grid is regenerated
[DEBUG  ] |  bcopt                = 5                                              # Boundary condition option
[DEBUG  ] |  eneopt               = 2                                              # Compute electrostatic energy and forces
[DEBUG  ] |  frcopt               = 0                                              # Output for computing electrostatic forces
[DEBUG  ] |  scalec               = 0                                              # Option to compute reaction field energy and forces
[DEBUG  ] |  cutfd                = 5.0                                            # Cutoff for finite-difference interactions
[DEBUG  ] |  cutnb                = 0.0                                            # Cutoff for nonbonded interations
[DEBUG  ] |  nsnba                = 1                                              # Sets how often atom-based pairlist is generated
[DEBUG  ] |  decompopt            = 2                                              # Option to select different decomposition schemes when INP = 2
[DEBUG  ] |  use_rmin             = 1                                              # The option to set up van der Waals radii
[DEBUG  ] |  sprob                = 0.557                                          # Solvent probe radius for SASA used to compute the dispersion term
[DEBUG  ] |  vprob                = 1.3                                            # Solvent probe radius for molecular volume (the volume enclosed by SASA)
[DEBUG  ] |  rhow_effect          = 1.129                                          # Effective water density used in the non-polar dispersion term calculation
[DEBUG  ] |  use_sav              = 1                                              # Use molecular volume (the volume enclosed by SASA) for cavity term calculation
[DEBUG  ] |  cavity_surften       = 0.0378                                         # Surface tension
[DEBUG  ] |  cavity_offset        = -0.5692                                        # Offset for nonpolar solvation calc
[DEBUG  ] |  maxsph               = 400                                            # Approximate number of dots to represent the maximum atomic solvent accessible surface
[DEBUG  ] |  maxarcdot            = 1500                                           # Number of dots used to store arc dots per atom
[DEBUG  ] |  npbverb              = 0                                              # Option to turn on verbose mode
[DEBUG  ] |/
[DEBUG  ] |
[DEBUG  ] |# Decomposition namelist variables
[DEBUG  ] |&decomposition
[DEBUG  ] |  idecomp              = 1                                              # Which type of decomposition analysis to do
[DEBUG  ] |  dec_verbose          = 0                                              # Control energy terms are printed to the output
[DEBUG  ] |  print_res            = "within 6"                                     # Which residues to print decomposition data for
[DEBUG  ] |  csv_format           = 1                                              # Write decomposition data in CSV format
[DEBUG  ] |/
[DEBUG  ] |
[DEBUG  ] |--------------------------------------------------------------
[DEBUG  ] 
[INFO   ] Checking mmpbsa.in input file...
[INFO   ] Checking mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/romi/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/romi/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/romi/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/romi/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /usr/local/gromacs/bin/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER topologies from GROMACS files...
[INFO   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[DEBUG  ] Running command: echo name 18 GMXMMPBSA_REC\n name 19 GMXMMPBSA_LIG\n  18 | 19\n q\n | /usr/local/gromacs/bin/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx
[DEBUG  ]                      :-) GROMACS - gmx make_ndx, 2021.5 (-:
[DEBUG  ] 
[DEBUG  ]                             GROMACS is written by:
[DEBUG  ]      Andrey Alekseenko              Emile Apol              Rossen Apostolov     
[DEBUG  ]          Paul Bauer           Herman J.C. Berendsen           Par Bjelkmar       
[DEBUG  ]        Christian Blau           Viacheslav Bolnykh             Kevin Boyd        
[DEBUG  ]      Aldert van Buuren           Rudi van Drunen             Anton Feenstra      
[DEBUG  ]     Gilles Gouaillardet             Alan Gray               Gerrit Groenhof      
[DEBUG  ]        Anca Hamuraru            Vincent Hindriksen          M. Eric Irrgang      
[DEBUG  ]       Aleksei Iupinov           Christoph Junghans             Joe Jordan        
[DEBUG  ]     Dimitrios Karkoulis            Peter Kasson                Jiri Kraus        
[DEBUG  ]       Carsten Kutzner              Per Larsson              Justin A. Lemkul     
[DEBUG  ]        Viveca Lindahl            Magnus Lundborg             Erik Marklund       
[DEBUG  ]         Pascal Merz             Pieter Meulenhoff            Teemu Murtola       
[DEBUG  ]         Szilard Pall               Sander Pronk              Roland Schulz       
[DEBUG  ]        Michael Shirts            Alexey Shvetsov             Alfons Sijbers      
[DEBUG  ]        Peter Tieleman              Jon Vincent              Teemu Virolainen     
[DEBUG  ]      Christian Wennberg            Maarten Wolf              Artem Zhmurov       
[DEBUG  ]                            and the project leaders:
[DEBUG  ]         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG  ] 
[DEBUG  ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG  ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG  ] Uppsala University, Stockholm University and
[DEBUG  ] the Royal Institute of Technology, Sweden.
[DEBUG  ] check out http://www.gromacs.org for more information.
[DEBUG  ] 
[DEBUG  ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG  ] under the terms of the GNU Lesser General Public License
[DEBUG  ] as published by the Free Software Foundation; either version 2.1
[DEBUG  ] of the License, or (at your option) any later version.
[DEBUG  ] 
[DEBUG  ] GROMACS:      gmx make_ndx, version 2021.5
[DEBUG  ] Executable:   /usr/local/gromacs/bin/gmx
[DEBUG  ] Data prefix:  /usr/local/gromacs
[DEBUG  ] Working dir:  /media/romi/My Book Duo/completed-simulation-oracle/auto-immune/rs3/completed/2xwt-rs3-310k/free-energy
[DEBUG  ] Command line:
[DEBUG  ]   gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx
[DEBUG  ] 
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "It's just the way this stuff is done" (Built to Spill)
[DEBUG  ] 
[DEBUG  ] Going to read 1 old index file(s)
[DEBUG  ] Counted atom numbers up to 133250 in index file
[DEBUG  ] 
[DEBUG  ]   0 System              : 133250 atoms
[DEBUG  ]   1 Protein             : 10255 atoms
[DEBUG  ]   2 Protein-H           :  5153 atoms
[DEBUG  ]   3 C-alpha             :   674 atoms
[DEBUG  ]   4 Backbone            :  2022 atoms
[DEBUG  ]   5 MainChain           :  2693 atoms
[DEBUG  ]   6 MainChain+Cb        :  3317 atoms
[DEBUG  ]   7 MainChain+H         :  3328 atoms
[DEBUG  ]   8 SideChain           :  6927 atoms
[DEBUG  ]   9 SideChain-H         :  2460 atoms
[DEBUG  ]  10 Prot-Masses         : 10255 atoms
[DEBUG  ]  11 non-Protein         : 122995 atoms
[DEBUG  ]  12 Water               : 122988 atoms
[DEBUG  ]  13 SOL                 : 122988 atoms
[DEBUG  ]  14 non-Water           : 10262 atoms
[DEBUG  ]  15 Ion                 :     7 atoms
[DEBUG  ]  16 CL                  :     7 atoms
[DEBUG  ]  17 Water_and_ions      : 122995 atoms
[DEBUG  ]  18 Chain_A             :  6455 atoms
[DEBUG  ]  19 Chain_B             :  3800 atoms
[DEBUG  ] 
[DEBUG  ]  nr : group      '!': not  'name' nr name   'splitch' nr    Enter: list groups
[DEBUG  ]  'a': atom       '&': and  'del' nr         'splitres' nr   'l': list residues
[DEBUG  ]  't': atom type  '|': or   'keep' nr        'splitat' nr    'h': help
[DEBUG  ]  'r': residue              'res' nr         'chain' char
[DEBUG  ]  "name": group             'case': case sensitive           'q': save and quit
[DEBUG  ]  'ri': residue index
[DEBUG  ] 
[DEBUG  ] > 
[DEBUG  ] 
[DEBUG  ] > 
[DEBUG  ] 
[DEBUG  ] > 
[DEBUG  ] Copied index group 18 'GMXMMPBSA_REC'
[DEBUG  ] Copied index group 19 'GMXMMPBSA_LIG'
[DEBUG  ] Merged two groups with OR: 6455 3800 -> 10255
[DEBUG  ] 
[DEBUG  ]  20 GMXMMPBSA_REC_GMXMMPBSA_LIG: 10255 atoms
[DEBUG  ] 
[DEBUG  ] > 
[INFO   ] Normal Complex: Saving group 18_19 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[DEBUG  ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /usr/local/gromacs/bin/gmx trjconv -f system_reduced.xtc -s md_0_10.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ]                      :-) GROMACS - gmx trjconv, 2021.5 (-:
[DEBUG  ] 
[DEBUG  ]                             GROMACS is written by:
[DEBUG  ]      Andrey Alekseenko              Emile Apol              Rossen Apostolov     
[DEBUG  ]          Paul Bauer           Herman J.C. Berendsen           Par Bjelkmar       
[DEBUG  ]        Christian Blau           Viacheslav Bolnykh             Kevin Boyd        
[DEBUG  ]      Aldert van Buuren           Rudi van Drunen             Anton Feenstra      
[DEBUG  ]     Gilles Gouaillardet             Alan Gray               Gerrit Groenhof      
[DEBUG  ]        Anca Hamuraru            Vincent Hindriksen          M. Eric Irrgang      
[DEBUG  ]       Aleksei Iupinov           Christoph Junghans             Joe Jordan        
[DEBUG  ]     Dimitrios Karkoulis            Peter Kasson                Jiri Kraus        
[DEBUG  ]       Carsten Kutzner              Per Larsson              Justin A. Lemkul     
[DEBUG  ]        Viveca Lindahl            Magnus Lundborg             Erik Marklund       
[DEBUG  ]         Pascal Merz             Pieter Meulenhoff            Teemu Murtola       
[DEBUG  ]         Szilard Pall               Sander Pronk              Roland Schulz       
[DEBUG  ]        Michael Shirts            Alexey Shvetsov             Alfons Sijbers      
[DEBUG  ]        Peter Tieleman              Jon Vincent              Teemu Virolainen     
[DEBUG  ]      Christian Wennberg            Maarten Wolf              Artem Zhmurov       
[DEBUG  ]                            and the project leaders:
[DEBUG  ]         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG  ] 
[DEBUG  ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG  ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG  ] Uppsala University, Stockholm University and
[DEBUG  ] the Royal Institute of Technology, Sweden.
[DEBUG  ] check out http://www.gromacs.org for more information.
[DEBUG  ] 
[DEBUG  ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG  ] under the terms of the GNU Lesser General Public License
[DEBUG  ] as published by the Free Software Foundation; either version 2.1
[DEBUG  ] of the License, or (at your option) any later version.
[DEBUG  ] 
[DEBUG  ] GROMACS:      gmx trjconv, version 2021.5
[DEBUG  ] Executable:   /usr/local/gromacs/bin/gmx
[DEBUG  ] Data prefix:  /usr/local/gromacs
[DEBUG  ] Working dir:  /media/romi/My Book Duo/completed-simulation-oracle/auto-immune/rs3/completed/2xwt-rs3-310k/free-energy
[DEBUG  ] Command line:
[DEBUG  ]   gmx trjconv -f system_reduced.xtc -s md_0_10.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ] 
[DEBUG  ] Will write pdb: Protein data bank file
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Group     0 (         System) has 133250 elements
[DEBUG  ] Group     1 (        Protein) has 10255 elements
[DEBUG  ] Group     2 (      Protein-H) has  5153 elements
[DEBUG  ] Group     3 (        C-alpha) has   674 elements
[DEBUG  ] Group     4 (       Backbone) has  2022 elements
[DEBUG  ] Group     5 (      MainChain) has  2693 elements
[DEBUG  ] Group     6 (   MainChain+Cb) has  3317 elements
[DEBUG  ] Group     7 (    MainChain+H) has  3328 elements
[DEBUG  ] Group     8 (      SideChain) has  6927 elements
[DEBUG  ] Group     9 (    SideChain-H) has  2460 elements
[DEBUG  ] Group    10 (    Prot-Masses) has 10255 elements
[DEBUG  ] Group    11 (    non-Protein) has 122995 elements
[DEBUG  ] Group    12 (          Water) has 122988 elements
[DEBUG  ] Group    13 (            SOL) has 122988 elements
[DEBUG  ] Group    14 (      non-Water) has 10262 elements
[DEBUG  ] Group    15 (            Ion) has     7 elements
[DEBUG  ] Group    16 (             CL) has     7 elements
[DEBUG  ] Group    17 ( Water_and_ions) has 122995 elements
[DEBUG  ] Group    18 (  GMXMMPBSA_REC) has  6455 elements
[DEBUG  ] Group    19 (  GMXMMPBSA_LIG) has  3800 elements
[DEBUG  ] Group    20 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 10255 elements
[DEBUG  ] Select a group: Reading frame       0 time    0.000   
[DEBUG  ] Precision of system_reduced.xtc is 0.001 (nm)
[DEBUG  ] Reading frame       1 time  100.000   Reading frame       0 time    0.000   
[DEBUG  ] Dumping frame at t= 0 ps
[DEBUG  ]  ->  frame      0 time    0.000      Reading frame       1 time  100.000   
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "It's just the way this stuff is done" (Built to Spill)
[DEBUG  ] 
[DEBUG  ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG  ] Select group for output
[DEBUG  ] Selected 20: 'GMXMMPBSA_REC_GMXMMPBSA_LIG'
[INFO   ] No receptor structure file was defined. Using ST approach...
[INFO   ] Using receptor structure from complex to generate AMBER topology
[INFO   ] Normal Receptor: Saving group 18 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[DEBUG  ] Running command: echo 18 | /usr/local/gromacs/bin/gmx trjconv -f system_reduced.xtc -s md_0_10.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ]                      :-) GROMACS - gmx trjconv, 2021.5 (-:
[DEBUG  ] 
[DEBUG  ]                             GROMACS is written by:
[DEBUG  ]      Andrey Alekseenko              Emile Apol              Rossen Apostolov     
[DEBUG  ]          Paul Bauer           Herman J.C. Berendsen           Par Bjelkmar       
[DEBUG  ]        Christian Blau           Viacheslav Bolnykh             Kevin Boyd        
[DEBUG  ]      Aldert van Buuren           Rudi van Drunen             Anton Feenstra      
[DEBUG  ]     Gilles Gouaillardet             Alan Gray               Gerrit Groenhof      
[DEBUG  ]        Anca Hamuraru            Vincent Hindriksen          M. Eric Irrgang      
[DEBUG  ]       Aleksei Iupinov           Christoph Junghans             Joe Jordan        
[DEBUG  ]     Dimitrios Karkoulis            Peter Kasson                Jiri Kraus        
[DEBUG  ]       Carsten Kutzner              Per Larsson              Justin A. Lemkul     
[DEBUG  ]        Viveca Lindahl            Magnus Lundborg             Erik Marklund       
[DEBUG  ]         Pascal Merz             Pieter Meulenhoff            Teemu Murtola       
[DEBUG  ]         Szilard Pall               Sander Pronk              Roland Schulz       
[DEBUG  ]        Michael Shirts            Alexey Shvetsov             Alfons Sijbers      
[DEBUG  ]        Peter Tieleman              Jon Vincent              Teemu Virolainen     
[DEBUG  ]      Christian Wennberg            Maarten Wolf              Artem Zhmurov       
[DEBUG  ]                            and the project leaders:
[DEBUG  ]         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG  ] 
[DEBUG  ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG  ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG  ] Uppsala University, Stockholm University and
[DEBUG  ] the Royal Institute of Technology, Sweden.
[DEBUG  ] check out http://www.gromacs.org for more information.
[DEBUG  ] 
[DEBUG  ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG  ] under the terms of the GNU Lesser General Public License
[DEBUG  ] as published by the Free Software Foundation; either version 2.1
[DEBUG  ] of the License, or (at your option) any later version.
[DEBUG  ] 
[DEBUG  ] GROMACS:      gmx trjconv, version 2021.5
[DEBUG  ] Executable:   /usr/local/gromacs/bin/gmx
[DEBUG  ] Data prefix:  /usr/local/gromacs
[DEBUG  ] Working dir:  /media/romi/My Book Duo/completed-simulation-oracle/auto-immune/rs3/completed/2xwt-rs3-310k/free-energy
[DEBUG  ] Command line:
[DEBUG  ]   gmx trjconv -f system_reduced.xtc -s md_0_10.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ] 
[DEBUG  ] Will write pdb: Protein data bank file
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Group     0 (         System) has 133250 elements
[DEBUG  ] Group     1 (        Protein) has 10255 elements
[DEBUG  ] Group     2 (      Protein-H) has  5153 elements
[DEBUG  ] Group     3 (        C-alpha) has   674 elements
[DEBUG  ] Group     4 (       Backbone) has  2022 elements
[DEBUG  ] Group     5 (      MainChain) has  2693 elements
[DEBUG  ] Group     6 (   MainChain+Cb) has  3317 elements
[DEBUG  ] Group     7 (    MainChain+H) has  3328 elements
[DEBUG  ] Group     8 (      SideChain) has  6927 elements
[DEBUG  ] Group     9 (    SideChain-H) has  2460 elements
[DEBUG  ] Group    10 (    Prot-Masses) has 10255 elements
[DEBUG  ] Group    11 (    non-Protein) has 122995 elements
[DEBUG  ] Group    12 (          Water) has 122988 elements
[DEBUG  ] Group    13 (            SOL) has 122988 elements
[DEBUG  ] Group    14 (      non-Water) has 10262 elements
[DEBUG  ] Group    15 (            Ion) has     7 elements
[DEBUG  ] Group    16 (             CL) has     7 elements
[DEBUG  ] Group    17 ( Water_and_ions) has 122995 elements
[DEBUG  ] Group    18 (  GMXMMPBSA_REC) has  6455 elements
[DEBUG  ] Group    19 (  GMXMMPBSA_LIG) has  3800 elements
[DEBUG  ] Group    20 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 10255 elements
[DEBUG  ] Select a group: Reading frame       0 time    0.000   
[DEBUG  ] Precision of system_reduced.xtc is 0.001 (nm)
[DEBUG  ] Reading frame       1 time  100.000   Reading frame       0 time    0.000   
[DEBUG  ] Dumping frame at t= 0 ps
[DEBUG  ]  ->  frame      0 time    0.000      Reading frame       1 time  100.000   
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "It's just the way this stuff is done" (Built to Spill)
[DEBUG  ] 
[DEBUG  ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG  ] Select group for output
[DEBUG  ] Selected 18: 'GMXMMPBSA_REC'
[INFO   ] No ligand structure file was defined. Using ST approach...
[INFO   ] Using ligand structure from complex to generate AMBER topology
[INFO   ] Normal Ligand: Saving group 19 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[DEBUG  ] Running command: echo 19 | /usr/local/gromacs/bin/gmx trjconv -f system_reduced.xtc -s md_0_10.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ]                      :-) GROMACS - gmx trjconv, 2021.5 (-:
[DEBUG  ] 
[DEBUG  ]                             GROMACS is written by:
[DEBUG  ]      Andrey Alekseenko              Emile Apol              Rossen Apostolov     
[DEBUG  ]          Paul Bauer           Herman J.C. Berendsen           Par Bjelkmar       
[DEBUG  ]        Christian Blau           Viacheslav Bolnykh             Kevin Boyd        
[DEBUG  ]      Aldert van Buuren           Rudi van Drunen             Anton Feenstra      
[DEBUG  ]     Gilles Gouaillardet             Alan Gray               Gerrit Groenhof      
[DEBUG  ]        Anca Hamuraru            Vincent Hindriksen          M. Eric Irrgang      
[DEBUG  ]       Aleksei Iupinov           Christoph Junghans             Joe Jordan        
[DEBUG  ]     Dimitrios Karkoulis            Peter Kasson                Jiri Kraus        
[DEBUG  ]       Carsten Kutzner              Per Larsson              Justin A. Lemkul     
[DEBUG  ]        Viveca Lindahl            Magnus Lundborg             Erik Marklund       
[DEBUG  ]         Pascal Merz             Pieter Meulenhoff            Teemu Murtola       
[DEBUG  ]         Szilard Pall               Sander Pronk              Roland Schulz       
[DEBUG  ]        Michael Shirts            Alexey Shvetsov             Alfons Sijbers      
[DEBUG  ]        Peter Tieleman              Jon Vincent              Teemu Virolainen     
[DEBUG  ]      Christian Wennberg            Maarten Wolf              Artem Zhmurov       
[DEBUG  ]                            and the project leaders:
[DEBUG  ]         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG  ] 
[DEBUG  ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG  ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG  ] Uppsala University, Stockholm University and
[DEBUG  ] the Royal Institute of Technology, Sweden.
[DEBUG  ] check out http://www.gromacs.org for more information.
[DEBUG  ] 
[DEBUG  ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG  ] under the terms of the GNU Lesser General Public License
[DEBUG  ] as published by the Free Software Foundation; either version 2.1
[DEBUG  ] of the License, or (at your option) any later version.
[DEBUG  ] 
[DEBUG  ] GROMACS:      gmx trjconv, version 2021.5
[DEBUG  ] Executable:   /usr/local/gromacs/bin/gmx
[DEBUG  ] Data prefix:  /usr/local/gromacs
[DEBUG  ] Working dir:  /media/romi/My Book Duo/completed-simulation-oracle/auto-immune/rs3/completed/2xwt-rs3-310k/free-energy
[DEBUG  ] Command line:
[DEBUG  ]   gmx trjconv -f system_reduced.xtc -s md_0_10.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ] 
[DEBUG  ] Will write pdb: Protein data bank file
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Group     0 (         System) has 133250 elements
[DEBUG  ] Group     1 (        Protein) has 10255 elements
[DEBUG  ] Group     2 (      Protein-H) has  5153 elements
[DEBUG  ] Group     3 (        C-alpha) has   674 elements
[DEBUG  ] Group     4 (       Backbone) has  2022 elements
[DEBUG  ] Group     5 (      MainChain) has  2693 elements
[DEBUG  ] Group     6 (   MainChain+Cb) has  3317 elements
[DEBUG  ] Group     7 (    MainChain+H) has  3328 elements
[DEBUG  ] Group     8 (      SideChain) has  6927 elements
[DEBUG  ] Group     9 (    SideChain-H) has  2460 elements
[DEBUG  ] Group    10 (    Prot-Masses) has 10255 elements
[DEBUG  ] Group    11 (    non-Protein) has 122995 elements
[DEBUG  ] Group    12 (          Water) has 122988 elements
[DEBUG  ] Group    13 (            SOL) has 122988 elements
[DEBUG  ] Group    14 (      non-Water) has 10262 elements
[DEBUG  ] Group    15 (            Ion) has     7 elements
[DEBUG  ] Group    16 (             CL) has     7 elements
[DEBUG  ] Group    17 ( Water_and_ions) has 122995 elements
[DEBUG  ] Group    18 (  GMXMMPBSA_REC) has  6455 elements
[DEBUG  ] Group    19 (  GMXMMPBSA_LIG) has  3800 elements
[DEBUG  ] Group    20 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 10255 elements
[DEBUG  ] Select a group: Reading frame       0 time    0.000   
[DEBUG  ] Precision of system_reduced.xtc is 0.001 (nm)
[DEBUG  ] Reading frame       1 time  100.000   Reading frame       0 time    0.000   
[DEBUG  ] Dumping frame at t= 0 ps
[DEBUG  ]  ->  frame      0 time    0.000      Reading frame       1 time  100.000   
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "It's just the way this stuff is done" (Built to Spill)
[DEBUG  ] 
[DEBUG  ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG  ] Select group for output
[DEBUG  ] Selected 19: 'GMXMMPBSA_LIG'
[INFO   ] Checking the structures consistency...
[INFO   ] 
[INFO   ] Using topology conversion. Setting radiopt = 0...
[INFO   ] Building Normal Complex Amber topology...
[INFO   ] Detected CHARMM force field topology format...
[INFO   ] Assigning PBRadii mbondi2 to Complex...
[INFO   ] Writing Normal Complex AMBER topology...
[INFO   ] No Receptor topology file was defined. Using ST approach...
[INFO   ] Building AMBER Receptor topology from Complex...
[INFO   ] Assigning PBRadii mbondi2 to Receptor...
[INFO   ] Writing Normal Receptor AMBER topology...
[INFO   ] No Ligand topology file was defined. Using ST approach...
[INFO   ] Building AMBER Ligand topology from Complex...
[INFO   ] Assigning PBRadii mbondi2 to Ligand...
[INFO   ] Writing Normal Ligand AMBER topology...
[INFO   ] Selecting residues by distance (6 Å) between receptor and ligand for decomposition analysis...
[INFO   ] Selected 105 residues:
R:A:VAL:2   R:A:GLY:26  R:A:TYR:27  R:A:SER:28  R:A:THR:30  R:A:ASP:31  R:A:ASN:32  R:A:TRP:33  R:A:TYR:52  R:A:GLY:54
R:A:ASP:55  R:A:SER:56  R:A:ASP:57  R:A:ARG:59  R:A:LYS:74  R:A:LEU:99  R:A:ASP:100 R:A:TRP:101 R:A:ASN:102 R:A:TYR:103
R:A:ASN:104 R:A:PRO:105 R:A:ARG:107 R:A:TYR:108 R:B:SER:246 R:B:SER:247 R:B:SER:248 R:B:ASP:249 R:B:ILE:250 R:B:GLY:251
R:B:SER:252 R:B:ASN:253 R:B:TYR:254 R:B:LEU:268 R:B:TYR:271 R:B:ASP:272 R:B:ASN:273 R:B:LYS:275 R:B:ARG:276 R:B:PRO:277
R:B:SER:278 R:B:ALA:279 R:B:LYS:288 R:B:THR:291 R:B:TRP:313 R:B:ASP:314 R:B:SER:315 R:B:ARG:316 R:B:LEU:317 R:B:GLY:318
R:B:ILE:319 L:C:GLU:448 L:C:GLU:449 L:C:ASP:450 L:C:PHE:451 L:C:ARG:452 L:C:THR:454 L:C:CYS:455 L:C:LYS:456 L:C:GLN:469
L:C:THR:470 L:C:LYS:472 L:C:ILE:474 L:C:GLU:475 L:C:ASN:491 L:C:ILE:492 L:C:SER:493 L:C:ARG:494 L:C:TYR:496 L:C:VAL:497
L:C:SER:498 L:C:ILE:499 L:C:LYS:516 L:C:VAL:517 L:C:THR:518 L:C:HIS:519 L:C:GLU:521 L:C:ARG:523 L:C:ASN:524 L:C:ARG:526
L:C:LEU:541 L:C:LYS:543 L:C:PHE:544 L:C:LEU:545 L:C:GLY:546 L:C:PHE:548 L:C:ASN:549 L:C:ASP:565 L:C:ILE:566 L:C:PHE:567
L:C:PHE:568 L:C:ILE:569 L:C:GLU:571 L:C:THR:573 L:C:ASP:574 L:C:GLU:592 L:C:THR:593 L:C:THR:595 L:C:LYS:597 L:C:TYR:599
L:C:ASP:617 L:C:ALA:618 L:C:TYR:620 L:C:SER:643 L:C:LEU:644

[INFO   ] Cleaning normal complex trajectories...
[DEBUG  ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /usr/local/gromacs/bin/gmx trjconv -f system_reduced.xtc -s md_0_10.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx
[DEBUG  ]                      :-) GROMACS - gmx trjconv, 2021.5 (-:
[DEBUG  ] 
[DEBUG  ]                             GROMACS is written by:
[DEBUG  ]      Andrey Alekseenko              Emile Apol              Rossen Apostolov     
[DEBUG  ]          Paul Bauer           Herman J.C. Berendsen           Par Bjelkmar       
[DEBUG  ]        Christian Blau           Viacheslav Bolnykh             Kevin Boyd        
[DEBUG  ]      Aldert van Buuren           Rudi van Drunen             Anton Feenstra      
[DEBUG  ]     Gilles Gouaillardet             Alan Gray               Gerrit Groenhof      
[DEBUG  ]        Anca Hamuraru            Vincent Hindriksen          M. Eric Irrgang      
[DEBUG  ]       Aleksei Iupinov           Christoph Junghans             Joe Jordan        
[DEBUG  ]     Dimitrios Karkoulis            Peter Kasson                Jiri Kraus        
[DEBUG  ]       Carsten Kutzner              Per Larsson              Justin A. Lemkul     
[DEBUG  ]        Viveca Lindahl            Magnus Lundborg             Erik Marklund       
[DEBUG  ]         Pascal Merz             Pieter Meulenhoff            Teemu Murtola       
[DEBUG  ]         Szilard Pall               Sander Pronk              Roland Schulz       
[DEBUG  ]        Michael Shirts            Alexey Shvetsov             Alfons Sijbers      
[DEBUG  ]        Peter Tieleman              Jon Vincent              Teemu Virolainen     
[DEBUG  ]      Christian Wennberg            Maarten Wolf              Artem Zhmurov       
[DEBUG  ]                            and the project leaders:
[DEBUG  ]         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG  ] 
[DEBUG  ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG  ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG  ] Uppsala University, Stockholm University and
[DEBUG  ] the Royal Institute of Technology, Sweden.
[DEBUG  ] check out http://www.gromacs.org for more information.
[DEBUG  ] 
[DEBUG  ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG  ] under the terms of the GNU Lesser General Public License
[DEBUG  ] as published by the Free Software Foundation; either version 2.1
[DEBUG  ] of the License, or (at your option) any later version.
[DEBUG  ] 
[DEBUG  ] GROMACS:      gmx trjconv, version 2021.5
[DEBUG  ] Executable:   /usr/local/gromacs/bin/gmx
[DEBUG  ] Data prefix:  /usr/local/gromacs
[DEBUG  ] Working dir:  /media/romi/My Book Duo/completed-simulation-oracle/auto-immune/rs3/completed/2xwt-rs3-310k/free-energy
[DEBUG  ] Command line:
[DEBUG  ]   gmx trjconv -f system_reduced.xtc -s md_0_10.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx
[DEBUG  ] 
[DEBUG  ] Will write xtc: Compressed trajectory (portable xdr format): xtc
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Group     0 (         System) has 133250 elements
[DEBUG  ] Group     1 (        Protein) has 10255 elements
[DEBUG  ] Group     2 (      Protein-H) has  5153 elements
[DEBUG  ] Group     3 (        C-alpha) has   674 elements
[DEBUG  ] Group     4 (       Backbone) has  2022 elements
[DEBUG  ] Group     5 (      MainChain) has  2693 elements
[DEBUG  ] Group     6 (   MainChain+Cb) has  3317 elements
[DEBUG  ] Group     7 (    MainChain+H) has  3328 elements
[DEBUG  ] Group     8 (      SideChain) has  6927 elements
[DEBUG  ] Group     9 (    SideChain-H) has  2460 elements
[DEBUG  ] Group    10 (    Prot-Masses) has 10255 elements
[DEBUG  ] Group    11 (    non-Protein) has 122995 elements
[DEBUG  ] Group    12 (          Water) has 122988 elements
[DEBUG  ] Group    13 (            SOL) has 122988 elements
[DEBUG  ] Group    14 (      non-Water) has 10262 elements
[DEBUG  ] Group    15 (            Ion) has     7 elements
[DEBUG  ] Group    16 (             CL) has     7 elements
[DEBUG  ] Group    17 ( Water_and_ions) has 122995 elements
[DEBUG  ] Group    18 (  GMXMMPBSA_REC) has  6455 elements
[DEBUG  ] Group    19 (  GMXMMPBSA_LIG) has  3800 elements
[DEBUG  ] Group    20 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 10255 elements
[DEBUG  ] Select a group: Reading frame       0 time    0.000   
[DEBUG  ] Precision of system_reduced.xtc is 0.001 (nm)
[DEBUG  ] Using output precision of 0.001 (nm)
[DEBUG  ]  ->  frame      0 time    0.000      Reading frame       1 time  100.000    ->  frame      1 time  100.000      Reading frame       2 time  200.000    ->  frame      2 time  200.000      Reading frame       3 time  300.000    ->  frame      3 time  300.000      Reading frame       4 time  400.000    ->  frame      4 time  400.000      Reading frame       5 time  500.000    ->  frame      5 time  500.000      Reading frame       6 time  600.000    ->  frame      6 time  600.000      Reading frame       7 time  700.000    ->  frame      7 time  700.000      Reading frame       8 time  800.000    ->  frame      8 time  800.000      Reading frame       9 time  900.000    ->  frame      9 time  900.000      Reading frame      10 time 1000.000    ->  frame     10 time 1000.000      Reading frame      11 time 1100.000   Reading frame      12 time 1200.000   Reading frame      13 time 1300.000   Reading frame      14 time 1400.000   Reading frame      15 time 1500.000   Reading frame      16 time 1600.000   Reading frame      17 time 1700.000   Reading frame      18 time 1800.000   Reading frame      19 time 1900.000   Reading frame      20 time 2000.000    ->  frame     20 time 2000.000      Reading frame      30 time 3000.000    ->  frame     30 time 3000.000      Reading frame      40 time 4000.000    ->  frame     40 time 4000.000      Reading frame      50 time 5000.000    ->  frame     50 time 5000.000      Reading frame      60 time 6000.000    ->  frame     60 time 6000.000      Reading frame      70 time 7000.000    ->  frame     70 time 7000.000      Reading frame      80 time 8000.000    ->  frame     80 time 8000.000      Reading frame      90 time 9000.000    ->  frame     90 time 9000.000      Reading frame     100 time 10000.000    ->  frame    100 time 10000.000      Reading frame     110 time 11000.000    ->  frame    110 time 11000.000      Reading frame     120 time 12000.000    ->  frame    120 time 12000.000      Reading frame     130 time 13000.000    ->  frame    130 time 13000.000      Reading frame     140 time 14000.000    ->  frame    140 time 14000.000      Reading frame     150 time 15000.000    ->  frame    150 time 15000.000      Reading frame     160 time 16000.000    ->  frame    160 time 16000.000      Reading frame     170 time 17000.000    ->  frame    170 time 17000.000      Reading frame     180 time 18000.000    ->  frame    180 time 18000.000      Reading frame     190 time 19000.000    ->  frame    190 time 19000.000      Reading frame     200 time 20000.000    ->  frame    200 time 20000.000       ->  frame    210 time 21000.000       ->  frame    220 time 22000.000       ->  frame    230 time 23000.000       ->  frame    240 time 24000.000       ->  frame    250 time 25000.000       ->  frame    260 time 26000.000       ->  frame    270 time 27000.000       ->  frame    280 time 28000.000       ->  frame    290 time 29000.000      Reading frame     300 time 30000.000    ->  frame    300 time 30000.000       ->  frame    310 time 31000.000       ->  frame    320 time 32000.000       ->  frame    330 time 33000.000       ->  frame    340 time 34000.000       ->  frame    350 time 35000.000       ->  frame    360 time 36000.000       ->  frame    370 time 37000.000       ->  frame    380 time 38000.000       ->  frame    390 time 39000.000      Reading frame     400 time 40000.000    ->  frame    400 time 40000.000       ->  frame    410 time 41000.000       ->  frame    420 time 42000.000       ->  frame    430 time 43000.000       ->  frame    440 time 44000.000       ->  frame    450 time 45000.000       ->  frame    460 time 46000.000       ->  frame    470 time 47000.000       ->  frame    480 time 48000.000       ->  frame    490 time 49000.000      Reading frame     500 time 50000.000    ->  frame    500 time 50000.000       ->  frame    510 time 51000.000       ->  frame    520 time 52000.000       ->  frame    530 time 53000.000       ->  frame    540 time 54000.000       ->  frame    550 time 55000.000       ->  frame    560 time 56000.000       ->  frame    570 time 57000.000       ->  frame    580 time 58000.000       ->  frame    590 time 59000.000      Reading frame     600 time 60000.000    ->  frame    600 time 60000.000       ->  frame    610 time 61000.000       ->  frame    620 time 62000.000       ->  frame    630 time 63000.000       ->  frame    640 time 64000.000       ->  frame    650 time 65000.000       ->  frame    660 time 66000.000       ->  frame    670 time 67000.000       ->  frame    680 time 68000.000       ->  frame    690 time 69000.000      Reading frame     700 time 70000.000    ->  frame    700 time 70000.000       ->  frame    710 time 71000.000       ->  frame    720 time 72000.000       ->  frame    730 time 73000.000       ->  frame    740 time 74000.000       ->  frame    750 time 75000.000       ->  frame    760 time 76000.000       ->  frame    770 time 77000.000       ->  frame    780 time 78000.000       ->  frame    790 time 79000.000      Reading frame     800 time 80000.000    ->  frame    800 time 80000.000       ->  frame    810 time 81000.000       ->  frame    820 time 82000.000       ->  frame    830 time 83000.000       ->  frame    840 time 84000.000       ->  frame    850 time 85000.000       ->  frame    860 time 86000.000       ->  frame    870 time 87000.000       ->  frame    880 time 88000.000       ->  frame    890 time 89000.000      Reading frame     900 time 90000.000    ->  frame    900 time 90000.000       ->  frame    910 time 91000.000       ->  frame    920 time 92000.000       ->  frame    930 time 93000.000       ->  frame    940 time 94000.000       ->  frame    950 time 95000.000       ->  frame    960 time 96000.000       ->  frame    970 time 97000.000       ->  frame    980 time 98000.000       ->  frame    990 time 99000.000      Reading frame    1000 time 100000.000    ->  frame   1000 time 100000.000       ->  frame   1010 time 101000.000       ->  frame   1020 time 102000.000       ->  frame   1030 time 103000.000       ->  frame   1040 time 104000.000       ->  frame   1050 time 105000.000       ->  frame   1060 time 106000.000       ->  frame   1070 time 107000.000       ->  frame   1080 time 108000.000       ->  frame   1090 time 109000.000      Reading frame    1100 time 110000.000    ->  frame   1100 time 110000.000       ->  frame   1110 time 111000.000       ->  frame   1120 time 112000.000       ->  frame   1130 time 113000.000       ->  frame   1140 time 114000.000       ->  frame   1150 time 115000.000       ->  frame   1160 time 116000.000       ->  frame   1170 time 117000.000       ->  frame   1180 time 118000.000       ->  frame   1190 time 119000.000      Reading frame    1200 time 120000.000    ->  frame   1200 time 120000.000       ->  frame   1210 time 121000.000       ->  frame   1220 time 122000.000       ->  frame   1230 time 123000.000       ->  frame   1240 time 124000.000       ->  frame   1250 time 125000.000       ->  frame   1260 time 126000.000       ->  frame   1270 time 127000.000       ->  frame   1280 time 128000.000       ->  frame   1290 time 129000.000      Reading frame    1300 time 130000.000    ->  frame   1300 time 130000.000       ->  frame   1310 time 131000.000       ->  frame   1320 time 132000.000       ->  frame   1330 time 133000.000       ->  frame   1340 time 134000.000       ->  frame   1350 time 135000.000       ->  frame   1360 time 136000.000       ->  frame   1370 time 137000.000       ->  frame   1380 time 138000.000       ->  frame   1390 time 139000.000      Reading frame    1400 time 140000.000    ->  frame   1400 time 140000.000       ->  frame   1410 time 141000.000       ->  frame   1420 time 142000.000       ->  frame   1430 time 143000.000       ->  frame   1440 time 144000.000       ->  frame   1450 time 145000.000       ->  frame   1460 time 146000.000       ->  frame   1470 time 147000.000       ->  frame   1480 time 148000.000       ->  frame   1490 time 149000.000      Reading frame    1500 time 150000.000    ->  frame   1500 time 150000.000       ->  frame   1510 time 151000.000       ->  frame   1520 time 152000.000       ->  frame   1530 time 153000.000       ->  frame   1540 time 154000.000       ->  frame   1550 time 155000.000       ->  frame   1560 time 156000.000       ->  frame   1570 time 157000.000       ->  frame   1580 time 158000.000       ->  frame   1590 time 159000.000      Reading frame    1600 time 160000.000    ->  frame   1600 time 160000.000       ->  frame   1610 time 161000.000       ->  frame   1620 time 162000.000       ->  frame   1630 time 163000.000       ->  frame   1640 time 164000.000       ->  frame   1650 time 165000.000       ->  frame   1660 time 166000.000       ->  frame   1670 time 167000.000       ->  frame   1680 time 168000.000       ->  frame   1690 time 169000.000      Reading frame    1700 time 170000.000    ->  frame   1700 time 170000.000       ->  frame   1710 time 171000.000       ->  frame   1720 time 172000.000       ->  frame   1730 time 173000.000       ->  frame   1740 time 174000.000       ->  frame   1750 time 175000.000       ->  frame   1760 time 176000.000       ->  frame   1770 time 177000.000       ->  frame   1780 time 178000.000       ->  frame   1790 time 179000.000      Reading frame    1800 time 180000.000    ->  frame   1800 time 180000.000       ->  frame   1810 time 181000.000       ->  frame   1820 time 182000.000       ->  frame   1830 time 183000.000       ->  frame   1840 time 184000.000       ->  frame   1850 time 185000.000       ->  frame   1860 time 186000.000       ->  frame   1870 time 187000.000       ->  frame   1880 time 188000.000       ->  frame   1890 time 189000.000      Reading frame    1900 time 190000.000    ->  frame   1900 time 190000.000       ->  frame   1910 time 191000.000       ->  frame   1920 time 192000.000       ->  frame   1930 time 193000.000       ->  frame   1940 time 194000.000       ->  frame   1950 time 195000.000       ->  frame   1960 time 196000.000       ->  frame   1970 time 197000.000       ->  frame   1980 time 198000.000       ->  frame   1990 time 199000.000      Reading frame    2000 time 200000.000    ->  frame   2000 time 200000.000      Last frame       2000 time 200000.000   
[DEBUG  ] 
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "The time for theory is over" (J. Hajdu)
[DEBUG  ] 
[DEBUG  ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG  ] Select group for output
[DEBUG  ] Selected 20: 'GMXMMPBSA_REC_GMXMMPBSA_LIG'
[INFO   ] Building AMBER topologies from GROMACS files... Done.

[INFO   ] Loading and checking parameter files for compatibility...
[INFO   ] Preparing trajectories for simulation...

[INFO   ] 20 frames were processed by cpptraj for use in calculation.
[INFO   ] Running calculations on normal system...
[INFO   ] Beginning GB calculations with /home/romi/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
[INFO   ]   calculating receptor contribution...
[INFO   ]   calculating ligand contribution...
[INFO   ] Beginning PB calculations with /home/romi/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
[INFO   ]   calculating receptor contribution...
[INFO   ]   calculating ligand contribution...
[INFO   ] Parsing results to output files...

[DEBUG  ] Creating converter from 5 to 3
[INFO   ] Timing:
[INFO   ] Total GROMACS setup time:                   0.370 min.
[INFO   ] Total AMBER setup time:                     0.014 min.
[INFO   ] Creating trajectories with cpptraj:         0.007 min.
[INFO   ] Total calculation time:                    54.378 min.
[INFO   ] Total GB calculation time:                  8.038 min.
[INFO   ] Total PB calculation time:                 46.340 min.
[INFO   ] Statistics calculation & output writing:    0.007 min.
[INFO   ] Total time taken:                          54.781 min.

[INFO   ] 
   Finalizing gmx_MMPBSA: [ERROR  ] = 0; [WARNING] = 0
   Check the gmx_MMPBSA.log file for more details...

[INFO   ] 
 Thank you for using gmx_MMPBSA. Please consider supporting gmx_MMPBSA by citing our publication:
    Valdés-Tresanco, M.S., Valdés-Tresanco, M.E., Valiente, P.A. and Moreno E. 
    gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS. 
    J Chem Theory Comput., 2021, 17 (10):6281-6291. Epub 2021 Sep 29. PMID: 34586825.
    https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645

Also consider citing MMPBSA.py:
    Miller III, B. R., McGee Jr., T. D., Swails, J. M. Homeyer, N. Gohlke, H. and Roitberg, A. E.
    MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
    J. Chem. Theory Comput., 2012, 8 (9) pp 3314-3321

[INFO   ] Opening gmx_MMPBSA_ana to analyze results...

[INFO   ] Finalized...
